Contacts of the helix formed by residues 333 - 350 (chain B) in PDB entry 3EE6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B PRO 5.1 0.2 - - - -
24B GLU* 2.6 45.1 + - - -
26B ASP* 3.7 21.5 + - - -
27B GLN* 3.0 16.1 + - - -
332B LEU* 1.3 76.7 - - - +
334B SER* 1.3 59.3 + - - +
335B ALA 3.7 2.2 + - - -
336B TYR* 3.0 20.7 + - - +
337B ILE* 3.0 28.3 + - - +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 3.0 20.8 + - - -
332B LEU 3.8 0.6 + - - -
333B SER* 1.3 72.7 - - - +
335B ALA* 1.3 57.4 + - - +
337B ILE* 4.0 9.0 - - - -
338B GLN* 2.9 47.9 + - - +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PRO 3.8 19.4 + - - +
24B GLU* 4.6 4.0 - - + -
26B ASP* 5.3 0.2 + - - -
168B ASP* 3.6 29.6 - - + +
169B PHE* 4.0 4.0 - - + -
333B SER* 3.2 5.4 + - - +
334B SER* 1.3 81.2 - - - +
336B TYR* 1.3 61.5 + - - +
338B GLN* 4.1 3.1 - - - +
339B ARG* 3.1 26.0 + - - +
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Residues in contact with TYR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLU* 4.0 2.2 - - - +
169B PHE* 3.8 24.4 - + + -
175B ARG* 3.2 46.1 + - - +
302B GLU* 4.0 7.5 + - - -
304B PHE* 3.8 27.0 - - - +
305B LEU* 4.7 10.7 + - + -
325B TYR* 4.9 8.3 + - - -
327B ASP* 5.2 2.3 + - - -
332B LEU* 4.0 35.9 - - + -
333B SER* 3.0 22.1 + - - +
335B ALA* 1.3 76.8 - - - +
337B ILE* 1.3 66.0 + - - +
339B ARG* 3.1 2.4 + - - +
340B VAL* 2.9 54.9 + - + +
378B PHE* 4.9 5.1 - + - -
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B GLU* 3.9 32.3 - - + +
332B LEU* 3.8 27.6 - - + +
333B SER 3.0 17.2 + - - +
334B SER* 3.5 14.6 - - - +
336B TYR* 1.3 81.4 - - - +
338B GLN* 1.3 71.2 + - - +
340B VAL 3.6 0.2 + - - -
341B ASN* 3.2 22.2 + - - +
378B PHE* 3.9 29.8 - - + -
415B VAL* 4.1 25.8 - - + -
416B PHE* 4.0 10.3 - - + -
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Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B SER* 2.9 35.6 + - - +
335B ALA* 4.2 3.1 - - - +
337B ILE* 1.3 81.9 - - + +
339B ARG* 1.3 61.7 + - - +
341B ASN* 3.4 9.4 + - - +
342B THR* 3.1 22.7 + - - -
415B VAL* 3.8 29.5 + - - +
416B PHE* 3.9 19.0 - - - -
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Residues in contact with ARG 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA* 3.6 12.7 - - + +
53B LEU 2.9 21.6 + - - -
55B GLN* 3.4 23.4 - - - +
118B ASP* 2.8 36.0 + - - +
119B PHE* 3.2 26.5 - - + -
168B ASP* 2.9 23.2 + - + +
169B PHE* 3.7 26.2 - - + -
305B LEU* 6.2 0.4 - - + -
335B ALA 3.1 20.4 + - - +
336B TYR 3.1 0.4 + - - +
338B GLN* 1.3 74.6 - - - +
340B VAL* 1.3 67.9 + - + +
342B THR* 3.1 4.5 + - - -
343B GLU* 2.8 42.4 + - + +
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PHE* 5.7 0.4 - - + -
304B PHE* 3.9 19.7 - - + -
305B LEU* 5.4 2.9 - - + -
308B LEU* 4.0 20.0 - - + -
336B TYR* 2.9 56.7 + - + +
337B ILE 4.0 0.2 - - - +
339B ARG* 1.3 76.5 - - + +
341B ASN* 1.3 65.1 + - - +
343B GLU* 2.9 14.8 + - - +
344B LEU* 2.9 23.6 + - + +
378B PHE* 3.5 28.5 - - + -
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ILE 3.2 12.2 + - - +
338B GLN* 3.4 13.7 + - - +
340B VAL* 1.3 81.0 - - - +
342B THR* 1.3 57.3 + - - +
344B LEU* 3.3 10.5 + - - +
345B MET* 3.0 29.9 + - - +
378B PHE* 4.3 1.5 - - + -
382B SER* 2.7 30.3 + - - -
383B PRO* 3.4 9.6 - - - +
384B TYR* 3.6 24.8 - - - -
416B PHE* 3.5 30.9 - - + -
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLN* 3.3 34.6 + - - +
58B VAL* 4.0 18.9 - - + +
61B LEU* 4.3 8.7 - - + -
89B VAL* 5.3 0.7 - - + -
338B GLN 3.1 13.0 + - - -
339B ARG* 3.1 12.3 + - - -
341B ASN* 1.3 74.0 + - - +
343B GLU* 1.3 65.8 + - - +
345B MET* 3.0 29.8 + - + +
346B LYS* 2.9 22.0 + - + +
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Residues in contact with GLU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLN* 3.1 13.2 + - - -
119B PHE* 3.3 24.4 - - + -
305B LEU* 6.2 0.2 - - + -
308B LEU* 3.6 38.5 - - + +
311B LEU* 5.8 2.1 - - - +
312B SER* 4.1 3.8 + - - -
339B ARG* 2.8 45.6 + - + +
340B VAL* 2.9 8.3 + - - +
342B THR* 1.3 74.4 - - - +
344B LEU* 1.3 64.0 + - - +
346B LYS* 3.1 35.6 + - - +
347B ALA* 3.1 19.9 + - - +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B PHE* 4.9 0.4 - - + -
308B LEU* 4.0 22.4 - - + -
311B LEU* 6.1 0.2 - - + -
340B VAL* 2.9 37.3 + - + +
341B ASN* 3.4 9.2 - - - +
342B THR 3.1 0.2 - - - -
343B GLU* 1.3 76.0 - - - +
345B MET* 1.3 63.6 + - - +
347B ALA* 3.1 15.3 + - - +
348B ALA* 3.1 14.0 + - - +
354B LEU* 3.9 19.5 - - + +
356B PHE* 4.7 11.9 - - + -
378B PHE* 4.5 3.1 - - + -
379B PRO* 4.5 7.9 - - + -
382B SER* 3.9 24.0 - - - +
384B TYR* 4.3 20.0 - - + +
385B VAL* 4.0 15.7 - - + -
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Residues in contact with MET 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL* 3.9 24.9 - - + +
61B LEU* 3.7 22.7 - - + -
62B SER* 3.6 22.4 - - - -
65B VAL* 3.3 17.0 - - + +
341B ASN* 3.0 16.2 + - - +
342B THR* 3.0 27.6 + - + +
344B LEU* 1.3 77.4 - - - +
346B LYS* 1.3 56.3 + - - +
348B ALA* 3.2 2.2 + - - +
349B ALA* 3.0 24.1 + - - +
384B TYR* 3.5 51.3 - - + +
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLN* 4.0 13.0 - - - +
61B LEU* 3.6 19.1 - - + -
85B VAL* 3.9 20.3 - - + +
89B VAL* 4.2 8.5 - - + -
116B THR* 3.2 26.3 + - - +
118B ASP* 2.7 26.3 + - - -
119B PHE* 4.8 0.2 - - - -
312B SER* 3.2 15.7 + - - -
342B THR* 2.9 20.7 + - + +
343B GLU* 3.1 30.9 + - - +
345B MET* 1.3 74.0 - - - +
347B ALA* 1.3 64.6 + - - +
349B ALA* 3.6 6.9 + - - +
350B ARG* 3.2 30.9 + - - +
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LEU* 4.8 6.7 - - + -
343B GLU 3.1 11.0 + - - +
344B LEU 3.1 9.8 + - - +
346B LYS* 1.3 77.8 - - - +
348B ALA* 1.3 61.9 + - - +
350B ARG* 3.1 14.0 + - - +
352B LEU* 3.1 41.0 + - + +
354B LEU* 3.5 32.8 - - + -
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B VAL* 3.8 18.4 - - + -
68B VAL* 4.0 11.6 - - - +
69B SER* 5.5 0.7 - - - -
79B TYR* 4.1 1.6 - - - -
344B LEU 3.1 11.0 + - - +
345B MET* 3.2 9.4 + - - +
347B ALA* 1.3 74.1 - - - +
349B ALA* 1.3 65.4 + - - +
351B GLY* 3.1 12.8 + - - -
352B LEU 4.1 11.0 - - - +
384B TYR* 5.0 6.7 - - + +
502B PHE* 3.5 33.5 + - + +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B LEU* 3.9 23.6 - - + -
64B LEU* 5.5 1.1 - - + -
65B VAL* 4.2 10.9 - - + +
68B VAL* 4.3 7.4 - - - +
79B TYR* 3.5 7.8 - - - +
80B LEU* 2.9 36.4 + - + +
85B VAL* 4.3 11.0 - - + -
345B MET 3.0 15.1 + - - +
346B LYS 3.8 7.4 - - - +
347B ALA 3.2 0.2 - - - -
348B ALA* 1.3 78.4 - - - +
350B ARG* 1.3 58.6 + - - +
351B GLY 3.2 1.1 + - - -
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Residues in contact with ARG 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TYR* 3.8 9.8 - - - +
80B LEU 3.3 21.4 - - - +
81B THR 4.5 0.7 - - - +
82B LEU* 3.4 31.8 - - - +
85B VAL* 3.8 16.4 - - + -
311B LEU* 2.8 28.9 + - - +
312B SER* 4.4 2.2 + - - +
314B GLU 3.0 23.6 + - - -
315B SER* 3.3 22.0 + - - +
317B LEU* 3.4 21.3 - - - +
346B LYS* 3.2 20.2 - - - +
347B ALA* 3.1 9.7 + - - +
349B ALA* 1.3 76.8 - - - +
351B GLY* 1.3 61.6 + - - +
352B LEU* 3.3 19.9 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il